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Yorodumi- PDB-7vpu: Crystal structure of the ligand-binding domain of L. thermotolera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vpu | ||||||
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Title | Crystal structure of the ligand-binding domain of L. thermotolerans Upc2 in complex with ergosterol | ||||||
Components | Sterol uptake control protein 2 (Upc2) | ||||||
Keywords | TRANSCRIPTION / ergosterol / transcription factor / ligand-binding / zinc finger | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity, RNA polymerase II-specific / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Lachancea thermotolerans CBS 6340 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Tan, L. / Im, Y.J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2022 Title: Structural basis for activation of fungal sterol receptor Upc2 and azole resistance. Authors: Tan, L. / Chen, L. / Yang, H. / Jin, B. / Kim, G. / Im, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vpu.cif.gz | 254.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vpu.ent.gz | 185.1 KB | Display | PDB format |
PDBx/mmJSON format | 7vpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/7vpu ftp://data.pdbj.org/pub/pdb/validation_reports/vp/7vpu | HTTPS FTP |
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-Related structure data
Related structure data | 7vprC 7vpsC 7vptC 7xb5C 4n9nS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37117.344 Da / Num. of mol.: 4 / Mutation: 587-600 deletion, S599V, M600D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lachancea thermotolerans CBS 6340 (fungus) Strain: CBS 6340 / Gene: KLTH0F07854g / Plasmid: pHIS2-Thr Details (production host): N-terminal cleavable hexa-histidine tag Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C5DKV6 #2: Chemical | ChemComp-ERG / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.6 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 0.1 M Na-Acetate pH 4.0, 15% PEG 20000, 0.2 M NaNO3 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→50 Å / Num. obs: 49148 / % possible obs: 99.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 58.87 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 33 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2446 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N9N Resolution: 2.59→24.31 Å / SU ML: 0.366 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.6909 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→24.31 Å
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Refine LS restraints |
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LS refinement shell |
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